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Source code for galaxy.tools.toolbox.panel

from abc import abstractmethod

from galaxy.util import bunch
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.odict import odict
from .parser import ensure_tool_conf_item

panel_item_types = bunch.Bunch(

[docs]class HasPanelItems: """ """
[docs] @abstractmethod def panel_items(self): """ Return an ordered dictionary-like object describing tool panel items (such as workflows, tools, labels, and sections). """
[docs] def panel_items_iter(self): """ Iterate through panel items each represented as a tuple of (panel_key, panel_type, panel_content). """ for panel_key, panel_value in self.panel_items().items(): if panel_value is None: continue panel_type = panel_item_types.SECTION if panel_key.startswith("tool_"): panel_type = panel_item_types.TOOL elif panel_key.startswith("label_"): panel_type = panel_item_types.LABEL elif panel_key.startswith("workflow_"): panel_type = panel_item_types.WORKFLOW yield (panel_key, panel_type, panel_value)
[docs]class ToolSection(Dictifiable, HasPanelItems): """ A group of tools with similar type/purpose that will be displayed as a group in the user interface. """ dict_collection_visible_keys = ['id', 'name', 'version']
[docs] def __init__(self, item=None): """ Build a ToolSection from an ElementTree element or a dictionary. """ if item is None: item = dict() self.name = item.get('name') or '' self.id = item.get('id') or '' self.version = item.get('version') or '' self.elems = ToolPanelElements()
[docs] def copy(self): copy = ToolSection() copy.name = self.name copy.id = self.id copy.version = self.version copy.elems = self.elems.copy() return copy
[docs] def to_dict(self, trans, link_details=False, tool_help=False, toolbox=None): """ Return a dict that includes section's attributes. """ section_dict = super().to_dict() section_elts = [] kwargs = dict( trans=trans, link_details=link_details, tool_help=tool_help ) for elt in self.elems.values(): if hasattr(elt, "tool_type") and toolbox: section_elts.append(toolbox.get_tool_to_dict(trans, elt, tool_help=tool_help)) else: section_elts.append(elt.to_dict(**kwargs)) section_dict['elems'] = section_elts return section_dict
[docs] def panel_items(self): return self.elems
[docs]class ToolSectionLabel(Dictifiable): """ A label for a set of tools that can be displayed above groups of tools and sections in the user interface """ dict_collection_visible_keys = ['id', 'text', 'version']
[docs] def __init__(self, item): """ Build a ToolSectionLabel from an ElementTree element or a dictionary. """ item = ensure_tool_conf_item(item) self.text = item.get("text") self.id = item.get("id") self.version = item.get("version") or ''
[docs] def to_dict(self, **kwds): return super().to_dict()
[docs]class ToolPanelElements(odict, HasPanelItems): """ Represents an ordered dictionary of tool entries - abstraction used both by tool panel itself (normal and integrated) and its sections. """
[docs] def update_or_append(self, index, key, value): if key in self or index is None: self[key] = value else: self.insert(index, key, value)
[docs] def get_label(self, label): for element in self.values(): if isinstance(element, ToolSection) and element.name == label: return element
[docs] def has_tool_with_id(self, tool_id): key = 'tool_%s' % tool_id return key in self
[docs] def replace_tool(self, previous_tool_id, new_tool_id, tool): previous_key = 'tool_%s' % previous_tool_id new_key = 'tool_%s' % new_tool_id index = self.keys().index(previous_key) del self[previous_key] self.insert(index, new_key, tool)
[docs] def index_of_tool_id(self, tool_id): query_key = 'tool_%s' % tool_id for index, target_key in enumerate(self.keys()): if query_key == target_key: return index return None
[docs] def insert_tool(self, index, tool): key = "tool_%s" % tool.id self.insert(index, key, tool)
[docs] def get_tool_with_id(self, tool_id): key = "tool_%s" % tool_id return self[key]
[docs] def append_tool(self, tool): key = "tool_%s" % tool.id self[key] = tool
[docs] def stub_tool(self, key): key = "tool_%s" % key self[key] = None
[docs] def stub_workflow(self, key): key = 'workflow_%s' % key self[key] = None
[docs] def stub_label(self, key): key = 'label_%s' % key self[key] = None
[docs] def append_section(self, key, section_elems): self[key] = section_elems
[docs] def panel_items(self): return self